Sure, you can calculate CFM from air meter velocity, but you have two things to watch out for. 1) Where do you put the air meter? I don't know how big your duct is, but velocity can vary in different parts of a duct. 2) If you are using an electronic, resistance type air meter it won't have this effect, but if you put in one of the propeller types in the ductwork, you can affect the dP in the system.
I think people like to use the pitot tube arrangement because it is cheap and reliable.